The 28-year-old midfielder recently pulled a muscle in his rib cage during a training session.
The Potters return to action on Sunday when they travel to Hull City in the Premier League.
"It's a disappointment to us because he is a good player and somebody we would prefer to have available to us," Hughes is quoted as saying by Sky Sports News.
"It looks like he will be out for a couple of weeks at least, or until the pain has gone to allow him to move around the pitch comfortably."
Stoke started their Premier League campaign last weekend with a 1-0 defeat at home to Aston Villa.